RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15137
(774 letters)
>gnl|CDD|212544 cd11681, HDAC_classIIa, Histone deacetylases, class IIa. Class IIa
histone deacetylases are Zn-dependent enzymes that
catalyze hydrolysis of N(6)-acetyl-lysine residues of
histones (EC 3.5.1.98) to yield deacetylated histones.
This subclass includes animal HDAC4, HDAC5, HDAC7, and
HDCA9. Histone acetylation/deacetylation process is
important for mediation of transcriptional regulation of
many genes. Histone deacetylases usually act via
association with DNA binding proteins to target specific
chromatin regions. Class IIa histone deacetylases are
signal-dependent co-repressors, they have N-terminal
regulatory domain with two or three conserved serine
residues, phosphorylation of these residues is important
for ability to shuttle between the nucleus and cytoplasm
and act as transcriptional co-repressors. HDAC9 is
involved in regulation of gene expression and dendritic
growth in developing cortical neurons. It also plays a
role in hematopoiesis. HDAC7 is involved in regulation
of myocyte migration and differentiation. HDAC5 is
involved in integration of chronic drug (cocaine)
addiction and depression with changes in chromatin
structure and gene expression. HDAC4 participates in
regulation of chondrocyte hypertrophy and
skeletogenesis.
Length = 377
Score = 405 bits (1044), Expect = e-135
Identities = 145/190 (76%), Positives = 164/190 (86%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGAL 592
WDVHHGNGTQQIFY D VLY+S+HR+DDGNFFPGTG P E G+GAG GFN+NIAWSG L
Sbjct: 188 WDVHHGNGTQQIFYEDPNVLYISLHRYDDGNFFPGTGAPTEVGSGAGEGFNVNIAWSGGL 247
Query: 593 NPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQ 652
+PPMGDAEYLAAFRT+VMP+A+EF P IVLVSAGFDAA GHPPPLGGYK+SPACFGYMT+
Sbjct: 248 DPPMGDAEYLAAFRTVVMPIAREFSPDIVLVSAGFDAAEGHPPPLGGYKVSPACFGYMTR 307
Query: 653 QLMTLADGKVVLALEGGYDLPSMCDSAEACVRALLGDAPPPLSQEELTRSPCLKAVETLQ 712
QLM LA GKVVLALEGGYDL ++CD++EACVRALLGD PLS+EEL R P AV +L+
Sbjct: 308 QLMNLAGGKVVLALEGGYDLTAICDASEACVRALLGDELDPLSEEELERRPNPNAVTSLE 367
Query: 713 KTIAIQVSHW 722
K IAIQ +W
Sbjct: 368 KVIAIQSPYW 377
Score = 72.8 bits (179), Expect = 2e-13
Identities = 24/32 (75%), Positives = 28/32 (87%)
Query: 486 PEQCGTGAGLGFNINIAWSGALNPPMGDAEYL 517
P + G+GAG GFN+NIAWSG L+PPMGDAEYL
Sbjct: 226 PTEVGSGAGEGFNVNIAWSGGLDPPMGDAEYL 257
>gnl|CDD|212531 cd10007, HDAC5, Histone deacetylase 5. Histone deacetylase 5 is a
class IIa Zn-dependent enzyme that catalyzes hydrolysis
of an N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. Class IIa histone deacetylases are
signal-dependent co-repressors, having N-terminal
regulatory domain with two or three conserved serine
residues; phosphorylation of these residues is important
for ability to shuttle between the nucleus and cytoplasm
and act as transcriptional co-repressors. HDAC5 is
involved in integration of chronic drug (cocaine)
addiction and depression with changes in chromatin
structure and gene expression; cocaine regulates HDAC5
function to antagonize the rewarding impact of cocaine,
possibly by blocking drug-stimulated gene expression
that supports drug-induced behavioral change. It is also
involved in regulation of angiogenesis and cell cycle as
well as immune system development. HDAC5 and HDAC9 have
been found to be significantly up-regulated in high-risk
medulloblastoma compared with low-risk and may
potentially be novel drug targets.
Length = 420
Score = 329 bits (845), Expect = e-105
Identities = 138/227 (60%), Positives = 172/227 (75%), Gaps = 4/227 (1%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGAL 592
WD+HHGNGTQQ FY+D VLY+S+HR+DDGNFFPG+G P E G G G+GFN+NIAW+G +
Sbjct: 191 WDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPDEVGAGPGVGFNVNIAWTGGV 250
Query: 593 NPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQ 652
+PP+GD EYL AFRT+VMP+A EF P +VLVSAGFDA GH PLGGY ++ CFG++T+
Sbjct: 251 DPPIGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYSVTAKCFGHLTK 310
Query: 653 QLMTLADGKVVLALEGGYDLPSMCDSAEACVRALLGDAPPPLSQEELTRSPCLKAVETLQ 712
QLMTLA G+VVLALEGG+DL ++CD++EACV ALLG PL L + P AV TL+
Sbjct: 311 QLMTLAGGRVVLALEGGHDLTAICDASEACVSALLGMELTPLDNTVLQQKPNDNAVATLE 370
Query: 713 KTIAIQVSHWPVLKRSAHTITWSALSA----AEDNETVSAMASLSMN 755
+ I IQ HW LKR A T+ +S L A E+ ETVSAMASLS++
Sbjct: 371 RVIEIQSKHWSCLKRFAATLGFSLLEAQRGELEEAETVSAMASLSVD 417
Score = 59.2 bits (143), Expect = 4e-09
Identities = 19/35 (54%), Positives = 29/35 (82%)
Query: 485 TPEQCGTGAGLGFNINIAWSGALNPPMGDAEYLSS 519
P++ G G G+GFN+NIAW+G ++PP+GD EYL++
Sbjct: 228 APDEVGAGPGVGFNVNIAWTGGVDPPIGDVEYLTA 262
>gnl|CDD|212530 cd10006, HDAC4, Histone deacetylase 4. Histone deacetylase 4 is a
class IIa Zn-dependent enzyme that catalyzes hydrolysis
of an N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. Class IIa histone deacetylases are
signal-dependent co-repressors, having N-terminal
regulatory domain with two or three conserved serine
residues; phosphorylation of these residues is important
for ability to shuttle between the nucleus and cytoplasm
and act as transcriptional co-repressors. HDAC4
participates in regulation of chondrocyte hypertrophy
and skeletogenesis. However, biological substrates for
HDAC4 have not been identified; only low lysine
deacetylation activity has been demonstrated and active
site mutant has enhanced activity toward acetylated
lysines. HDAC4 does not bind DNA directly, but through
transcription factors MEF2C (myocyte enhancer factor-2C)
and MEF2D. Other known interaction partners of the
protein are 14-3-3 proteins, SMRT and N-CoR
co-repressors, BCL6, HP1, SUMO-1 ubiquitin-like protein,
and ANKRA2. It appears to interact in a multiprotein
complex with RbAp48 and HDAC3. Furthermore, HDAC4 is
required for TGFbeta1-induced myofibroblastic
differentiation.
Length = 409
Score = 311 bits (798), Expect = 8e-99
Identities = 130/219 (59%), Positives = 168/219 (76%), Gaps = 4/219 (1%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGAL 592
WDVHHGNGTQQ FYSD VLY+S+HR+DDGNFFPG+G P E GTG G+GFN+N+A++G L
Sbjct: 191 WDVHHGNGTQQAFYSDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGL 250
Query: 593 NPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQ 652
+PPMGDAEYLAAFRT+VMP+A EF P +VLVS+GFDA GHP PLGGY LS CFGY+T+
Sbjct: 251 DPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTK 310
Query: 653 QLMTLADGKVVLALEGGYDLPSMCDSAEACVRALLGDAPPPLSQEELTRSPCLKAVETLQ 712
QLM LA G++VLALEGG+DL ++CD++EACV ALLG+ PL ++ L + P AV +++
Sbjct: 311 QLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSME 370
Query: 713 KTIAIQVSHWPVLKRSAHTITWSALSAA----EDNETVS 747
K + I +W L+R+ T +S + A E+ ETV+
Sbjct: 371 KVMEIHSKYWRCLQRTTSTAGYSLIEAQTCENEEAETVT 409
Score = 58.9 bits (142), Expect = 5e-09
Identities = 21/34 (61%), Positives = 31/34 (91%)
Query: 486 PEQCGTGAGLGFNINIAWSGALNPPMGDAEYLSS 519
P++ GTG G+GFN+N+A++G L+PPMGDAEYL++
Sbjct: 229 PDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAA 262
>gnl|CDD|212532 cd10008, HDAC7, Histone deacetylase 7. Histone deacetylase 7 is a
class IIa Zn-dependent enzyme that catalyzes hydrolysis
of an N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. Class IIa histone deacetylases are
signal-dependent co-repressors, having N-terminal
regulatory domain with two or three conserved serine
residues; phosphorylation of these residues is important
for ability to shuttle between the nucleus and cytoplasm
and act as transcriptional co-repressors. HDAC7 is
involved in regulation of myocyte migration and
differentiation. Known interaction partners of class IIa
HDAC7 are myocyte enhancer factors - MEF2A, -2C, and
-2D, 14-3-3 proteins, SMRT and N-CoR co-repressors,
HDAC3, ETA (endothelin receptor). This enzyme is also
involved in the development of the immune system as well
as brain and heart development. Multiple alternatively
spliced transcript variants encoding several isoforms
have been found for this gene.
Length = 378
Score = 304 bits (780), Expect = 2e-96
Identities = 123/190 (64%), Positives = 149/190 (78%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGAL 592
WDVHHGNGTQQ FY D VLY+S+HRHDDGNFFPG+G E G G+G GFN+N+AW+G L
Sbjct: 189 WDVHHGNGTQQTFYQDPSVLYISLHRHDDGNFFPGSGAVDEVGAGSGEGFNVNVAWAGGL 248
Query: 593 NPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQ 652
+PPMGD EYLAAFR +VMP+A+EF P +VLVSAGFDAA GHP PLGGY +S CFGYMTQ
Sbjct: 249 DPPMGDPEYLAAFRIVVMPIAREFSPDLVLVSAGFDAAEGHPAPLGGYHVSAKCFGYMTQ 308
Query: 653 QLMTLADGKVVLALEGGYDLPSMCDSAEACVRALLGDAPPPLSQEELTRSPCLKAVETLQ 712
QLM LA G VVLALEGG+DL ++CD++EACV ALLG+ PLS+E + P L A+ +L+
Sbjct: 309 QLMNLAGGAVVLALEGGHDLTAICDASEACVAALLGNEVDPLSEESWKQKPNLNAIRSLE 368
Query: 713 KTIAIQVSHW 722
I + +W
Sbjct: 369 AVIRVHSKYW 378
Score = 55.4 bits (133), Expect = 5e-08
Identities = 19/33 (57%), Positives = 28/33 (84%)
Query: 487 EQCGTGAGLGFNINIAWSGALNPPMGDAEYLSS 519
++ G G+G GFN+N+AW+G L+PPMGD EYL++
Sbjct: 228 DEVGAGSGEGFNVNVAWAGGLDPPMGDPEYLAA 260
>gnl|CDD|212533 cd10009, HDAC9, Histone deacetylase 9. Histone deacetylase 9 is a
class IIa Zn-dependent enzyme that catalyzes hydrolysis
of an N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. Class IIa histone deacetylases are
signal-dependent co-repressors, they have N-terminal
regulatory domain with two or three conserved serine
residues, phosphorylation of these residues is important
for ability to shuttle between the nucleus and cytoplasm
and act as transcriptional co-repressors. HDAC9 is
involved in regulation of gene expression and dendritic
growth in developing cortical neurons. It also plays a
role in hematopoiesis. Its deregulated expression may be
associated with some human cancers. HDAC5 and HDAC9 have
been found to be significantly up-regulated in high-risk
medulloblastoma compared with low-risk and may
potentially be novel drug targets.
Length = 379
Score = 295 bits (756), Expect = 6e-93
Identities = 127/189 (67%), Positives = 157/189 (83%)
Query: 534 DVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGALN 593
DVHHGNGTQQ FY+D +LY+S+HR+D+GNFFPG+G P E GTG G G+NINIAW+G L+
Sbjct: 190 DVHHGNGTQQAFYADPSILYISLHRYDEGNFFPGSGAPNEVGTGLGEGYNINIAWTGGLD 249
Query: 594 PPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQQ 653
PPMGD EYL AFRTIV PVAKEFDP +VLVSAGFDA GH PPLGGYK++ CFG++T+Q
Sbjct: 250 PPMGDVEYLEAFRTIVKPVAKEFDPDMVLVSAGFDALEGHTPPLGGYKVTAKCFGHLTKQ 309
Query: 654 LMTLADGKVVLALEGGYDLPSMCDSAEACVRALLGDAPPPLSQEELTRSPCLKAVETLQK 713
LMTLADG+VVLALEGG+DL ++CD++EACV ALLG+ PL+++ L +SP + AV +LQK
Sbjct: 310 LMTLADGRVVLALEGGHDLTAICDASEACVNALLGNELEPLAEDILHQSPNMNAVISLQK 369
Query: 714 TIAIQVSHW 722
I IQ +W
Sbjct: 370 IIEIQSKYW 378
Score = 59.3 bits (143), Expect = 3e-09
Identities = 22/34 (64%), Positives = 27/34 (79%)
Query: 486 PEQCGTGAGLGFNINIAWSGALNPPMGDAEYLSS 519
P + GTG G G+NINIAW+G L+PPMGD EYL +
Sbjct: 227 PNEVGTGLGEGYNINIAWTGGLDPPMGDVEYLEA 260
>gnl|CDD|212527 cd10003, HDAC6-dom2, Histone deacetylase 6, domain 2. Histone
deacetylase 6 is a class IIb Zn-dependent enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDACs usually act via association with DNA
binding proteins to target specific chromatin regions.
HDAC6 is the only histone deacetylase with internal
duplication of two catalytic domains which appear to
function independently of each other, and also has a
C-terminal ubiquitin-binding domain. It is located in
the cytoplasm and associates with microtubule motor
complex, functioning as the tubulin deacetylase and
regulating microtubule-dependent cell motility. Known
interaction partners of HDAC6 are alpha tubulin and
ubiquitin-like modifier FAT10 (also known as Ubiquitin D
or UBD).
Length = 350
Score = 269 bits (689), Expect = 2e-83
Identities = 97/196 (49%), Positives = 135/196 (68%), Gaps = 10/196 (5%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGT--GGPIECGTGAGLGFNINIAWSG 590
WDVHHGNGTQ +F SD VLY+S+HR+D+G+FFP + G G G G GFN+NI W+
Sbjct: 163 WDVHHGNGTQHMFESDPSVLYISLHRYDNGSFFPNSPEGNYDVVGKGKGEGFNVNIPWNK 222
Query: 591 ALNPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYM 650
MGDAEY+AAF+ +V+P+A EF+P++VLVSAGFDAA G P LGG K++P + +M
Sbjct: 223 ---GGMGDAEYIAAFQQVVLPIAYEFNPELVLVSAGFDAARGDP--LGGCKVTPEGYAHM 277
Query: 651 TQQLMTLADGKVVLALEGGYDLPSMCDSAEACVRALLGDAPPPLSQEELTRSPCLKAVET 710
T LM+LA G+V++ LEGGY+L S+ +S C + LLGD PP L +L R PC A+++
Sbjct: 278 THMLMSLAGGRVIVILEGGYNLTSISESMSMCTKTLLGDPPPVL---DLPRPPCSSALKS 334
Query: 711 LQKTIAIQVSHWPVLK 726
+ + + +W L+
Sbjct: 335 INNVLQVHQKYWKSLR 350
Score = 44.6 bits (106), Expect = 1e-04
Identities = 15/29 (51%), Positives = 19/29 (65%), Gaps = 3/29 (10%)
Query: 490 GTGAGLGFNINIAWSGALNPPMGDAEYLS 518
G G G GFN+NI W+ MGDAEY++
Sbjct: 207 GKGKGEGFNVNIPWNK---GGMGDAEYIA 232
>gnl|CDD|212518 cd09992, HDAC_classII, Histone deacetylases and histone-like
deacetylases, classII. Class II histone deacetylases
are Zn-dependent enzymes that catalyze hydrolysis of
N(6)-acetyl-lysine residues of histones (EC 3.5.1.98)
and possibly other proteins to yield deacetylated
histones/other proteins. This group includes animal
HDAC4,5,6,7,8,9,10, fungal HOS3 and HDA1, plant HDA5 and
HDA15 as well as other eukaryotes, archaeal and
bacterial histone-like deacetylases. Eukaryotic
deacetylases mostly use histones (H2, H3, H4) as
substrates for deacetylation; however, non-histone
substrates are known (for example, tubulin). Substrates
for prokaryotic histone-like deacetylases are not known.
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. Histone deacetylases usually act via association
with DNA binding proteins to target specific chromatin
regions. Interaction partners of class II deacetylases
include 14-3-3 proteins, MEF2 family of transcriptional
factors, CtBP, calmodulin (CaM), SMRT, N-CoR, BCL6,
HP1alpha and SUMO. Histone deacetylases play a role in
the regulation of cell cycle, cell differentiation and
survival. Class II mammalian HDACs are differentially
inhibited by structurally diverse compounds with known
antitumor activities, thus presenting them as potential
drug targets for human diseases resulting from aberrant
acetylation.
Length = 291
Score = 246 bits (630), Expect = 1e-75
Identities = 83/159 (52%), Positives = 104/159 (65%), Gaps = 13/159 (8%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGAL 592
WDVHHGNGTQ IFY D VLY SIH++ F+PGTG E G GAG GF IN+
Sbjct: 142 WDVHHGNGTQDIFYDDPSVLYFSIHQYP---FYPGTGAAEETGGGAGEGFTINVPLP--- 195
Query: 593 NPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQ 652
P GDAEYLAAF +++P+A+EF P +VLVSAGFDA G PLGG L+P + +T+
Sbjct: 196 -PGSGDAEYLAAFEEVLLPIAREFQPDLVLVSAGFDAHRGD--PLGGMNLTPEGYARLTR 252
Query: 653 QLMTLAD----GKVVLALEGGYDLPSMCDSAEACVRALL 687
L LAD G++V LEGGY+L ++ +S A + ALL
Sbjct: 253 LLKELADEHCGGRLVFVLEGGYNLEALAESVLAVLEALL 291
Score = 40.2 bits (95), Expect = 0.002
Identities = 16/32 (50%), Positives = 18/32 (56%), Gaps = 4/32 (12%)
Query: 486 PEQCGTGAGLGFNINIAWSGALNPPMGDAEYL 517
E+ G GAG GF IN+ P GDAEYL
Sbjct: 177 AEETGGGAGEGFTINVPLP----PGSGDAEYL 204
>gnl|CDD|212542 cd11600, HDAC_Clr3, Class II Histone deacetylase Clr3 and similar
proteins. Clr3 is a class II Histone deacetylase
Zn-dependent enzyme that catalyzes hydrolysis of an
N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Clr3 is the homolog
of the class-II HDAC HdaI in S. cerevisiae, and is
essential for silencing in heterochromatin regions, such
as centromeric regions, ribosomal DNA, the mating-type
region and telomeric loci. Clr3 has also been implicated
in the regulation of stress-related genes; the histone
acetyltransferase, Gcn5, in S. cerevisiae,
preferentially acetylates global histone H3K14 while
Clr3 preferentially deacetylates H3K14ac, and therefore,
interplay between Gcn5 and Clr3 is crucial for the
regulation of many stress-response genes.
Length = 313
Score = 246 bits (631), Expect = 2e-75
Identities = 91/165 (55%), Positives = 118/165 (71%), Gaps = 7/165 (4%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGT--GGPIECGTGAGLGFNINIAWSG 590
WD+HHGNGTQ+ FY D VLY+S+HR ++G F+PGT G G GAGLGFN+NI W
Sbjct: 154 WDIHHGNGTQRAFYDDPNVLYISLHRFENGGFYPGTPYGDYESVGEGAGLGFNVNIPWP- 212
Query: 591 ALNPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYM 650
MGDA+Y+ AF+ IVMP+A EFDP +V++SAGFDAA G LG ++PA + +M
Sbjct: 213 --QGGMGDADYIYAFQRIVMPIAYEFDPDLVIISAGFDAADGDE--LGQCHVTPAGYAHM 268
Query: 651 TQQLMTLADGKVVLALEGGYDLPSMCDSAEACVRALLGDAPPPLS 695
T LM+LA GK+V+ALEGGY+L ++ DSA A + LLG+APP L
Sbjct: 269 THMLMSLAGGKLVVALEGGYNLDAISDSALAVAKVLLGEAPPKLP 313
Score = 47.3 bits (113), Expect = 1e-05
Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 3/31 (9%)
Query: 487 EQCGTGAGLGFNINIAWSGALNPPMGDAEYL 517
E G GAGLGFN+NI W MGDA+Y+
Sbjct: 195 ESVGEGAGLGFNVNIPWP---QGGMGDADYI 222
>gnl|CDD|216151 pfam00850, Hist_deacetyl, Histone deacetylase domain. Histones can
be reversibly acetylated on several lysine residues.
Regulation of transcription is caused in part by this
mechanism. Histone deacetylases catalyze the removal of
the acetyl group. Histone deacetylases are related to
other proteins.
Length = 300
Score = 215 bits (550), Expect = 6e-64
Identities = 81/158 (51%), Positives = 100/158 (63%), Gaps = 12/158 (7%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGAL 592
DVHHGNGTQ+IFY D RVL +SIH+ F+PGTG E G GAG G+ +NI L
Sbjct: 152 LDVHHGNGTQEIFYDDPRVLTISIHQDP---FYPGTGFADETGEGAGEGYTLNI----PL 204
Query: 593 NPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQ 652
P GD EYLAAF I++P +EF P ++LVSAGFDA AG PLGG L+ + T+
Sbjct: 205 PPGTGDEEYLAAFEEILLPALREFQPDLILVSAGFDAHAGD--PLGGLNLTTEGYAERTR 262
Query: 653 QLMTLAD---GKVVLALEGGYDLPSMCDSAEACVRALL 687
L+ LAD G VV LEGGY+L ++ SA A + LL
Sbjct: 263 LLLELADAYGGPVVSVLEGGYNLDALARSAAAVLAGLL 300
Score = 34.9 bits (81), Expect = 0.12
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 486 PEQCGTGAGLGFNINIAWSGALNPPMGDAEYLS 518
++ G GAG G+ +NI L P GD EYL+
Sbjct: 187 ADETGEGAGEGYTLNI----PLPPGTGDEEYLA 215
>gnl|CDD|212526 cd10002, HDAC10_HDAC6-dom1, Histone deacetylase 6, domain 1 and
histone deacetylase 10. Histone deacetylases 6 and 10
are class IIb Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
HDACs usually act via association with DNA binding
proteins to target specific chromatin regions. HDAC6 is
the only histone deacetylase with internal duplication
of two catalytic domains which appear to function
independently of each other, and also has a C-terminal
ubiquitin-binding domain. It is located in the cytoplasm
and associates with microtubule motor complex,
functioning as the tubulin deacetylase and regulating
microtubule-dependent cell motility. HDAC10 has an
N-terminal deacetylase domain and a C-terminal
pseudo-repeat that shares significant similarity with
its catalytic domain. It is located in the nucleus and
cytoplasm, and is involved in regulation of
melanogenesis. It transcriptionally down-regulates
thioredoxin-interacting protein (TXNIP), leading to
altered reactive oxygen species (ROS) signaling in human
gastric cancer cells. Known interaction partners of
HDAC6 are alpha tubulin (substrate) and ubiquitin-like
modifier FAT10 (also known as Ubiquitin D or UBD) while
interaction partners of HDAC10 are Pax3, KAP1, hsc70 and
HDAC3 proteins.
Length = 336
Score = 215 bits (550), Expect = 2e-63
Identities = 88/192 (45%), Positives = 116/192 (60%), Gaps = 11/192 (5%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGP--IECGTGAGLGFNINIAWSG 590
WDVHHG GTQQ FY D RVLY SIHR++ G F+P G G G GFN+N+ +
Sbjct: 154 WDVHHGQGTQQGFYEDPRVLYFSIHRYEHGRFWPHLFESDYDYIGVGHGYGFNVNVPLNQ 213
Query: 591 ALNPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYM 650
+GDA+YLA F I++P+A EF P++VLVSAGFDA+ G P G ++PA + ++
Sbjct: 214 TG---LGDADYLAIFHHILLPLALEFQPELVLVSAGFDASIGDP--EGEMAVTPAGYAHL 268
Query: 651 TQQLMTLADGKVVLALEGGYDLPSMCDSAEACVRALLGDAPPPLSQEELTRSPCLKAVET 710
T+ LM LA GK++L LEGGY L S+ +S +R LLGD PPL+ P +ET
Sbjct: 269 TRLLMGLAGGKLLLVLEGGYLLESLAESVSMTLRGLLGDPLPPLAPP----IPIRSVLET 324
Query: 711 LQKTIAIQVSHW 722
+ IA W
Sbjct: 325 ILNAIAHLSPRW 336
Score = 35.4 bits (82), Expect = 0.091
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 481 LFERTPEQCGTGAGLGFNINIAWSGALNPPMGDAEYLS 518
LFE + G G G GFN+N+ + +GDA+YL+
Sbjct: 189 LFESDYDYIGVGHGYGFNVNVPLNQTG---LGDADYLA 223
>gnl|CDD|212545 cd11682, HDAC6-dom1, Histone deacetylase 6, domain 1. Histone
deacetylases 6 are class IIb Zn-dependent enzymes that
catalyze hydrolysis of N(6)-acetyl-lysine of a histone
to yield a deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
HDACs usually act via association with DNA binding
proteins to target specific chromatin regions. HDAC6 is
the only histone deacetylase with internal duplication
of two catalytic domains which appear to function
independently of each other, and also has a C-terminal
ubiquitin-binding domain. It is located in the cytoplasm
and associates with microtubule motor complex,
functioning as the tubulin deacetylase and regulating
microtubule-dependent cell motility. Known interaction
partners of HDAC6 are alpha tubulin (substrate) and
ubiquitin-like modifier FAT10 (also known as Ubiquitin D
or UBD).
Length = 337
Score = 195 bits (496), Expect = 5e-56
Identities = 89/192 (46%), Positives = 118/192 (61%), Gaps = 10/192 (5%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFP--GTGGPIECGTGAGLGFNINIAWSG 590
WDVHHG GTQ IF D VLY SIHR++ G F+P G G G G+NIN+ W+
Sbjct: 154 WDVHHGQGTQFIFEQDPSVLYFSIHRYEQGRFWPHLKESDSSAVGFGRGEGYNINVPWNQ 213
Query: 591 ALNPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYM 650
M DA+Y+AAF +++PVA EF PQ+VLV+AGFDA G P G +PACF ++
Sbjct: 214 V---GMRDADYIAAFLHVLLPVALEFQPQLVLVAAGFDAVIGDPK--GEMAATPACFAHL 268
Query: 651 TQQLMTLADGKVVLALEGGYDLPSMCDSAEACVRALLGDAPPPLSQEELTRSPCLKAVET 710
T LM LA GK++L+LEGGY+L S+ + A ++ALLGD P L E +PC A+ +
Sbjct: 269 THLLMGLAGGKLILSLEGGYNLRSLAEGVCASLKALLGDPCPML---ESPGAPCRSALAS 325
Query: 711 LQKTIAIQVSHW 722
+ TI+ W
Sbjct: 326 VSCTISALEPFW 337
Score = 32.5 bits (74), Expect = 0.91
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 490 GTGAGLGFNINIAWSGALNPPMGDAEYLSS 519
G G G G+NIN+ W+ M DA+Y+++
Sbjct: 198 GFGRGEGYNINVPWNQV---GMRDADYIAA 224
>gnl|CDD|212546 cd11683, HDAC10, Histone deacetylase 10. Histone deacetylases 10
are class IIb Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
HDACs usually act via association with DNA binding
proteins to target specific chromatin regions. HDAC10
has an N-terminal deacetylase domain and a C-terminal
pseudo-repeat that shares significant similarity with
its catalytic domain. It is located in the nucleus and
cytoplasm, and is involved in regulation of
melanogenesis. It transcriptionally down-regulates
thioredoxin-interacting protein (TXNIP), leading to
altered reactive oxygen species (ROS) signaling in human
gastric cancer cells. Known interaction partners of
HDAC10 are Pax3, KAP1, hsc70 and HDAC3 proteins.
Length = 337
Score = 185 bits (470), Expect = 2e-52
Identities = 90/192 (46%), Positives = 116/192 (60%), Gaps = 10/192 (5%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPG--TGGPIECGTGAGLGFNINIAWSG 590
WDVHHG G Q IF D VLY S HR++ F+P G G GLGFNIN+ W+
Sbjct: 154 WDVHHGQGIQYIFEEDPSVLYFSWHRYEHQRFWPFLRESDYDAVGRGKGLGFNINLPWNK 213
Query: 591 ALNPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYM 650
MG+A+YLAAF +++P+A EFDP++VLVSAGFD+A G P G +P CF ++
Sbjct: 214 V---GMGNADYLAAFFHVLLPLAFEFDPELVLVSAGFDSAIGDPE--GQMCATPECFAHL 268
Query: 651 TQQLMTLADGKVVLALEGGYDLPSMCDSAEACVRALLGDAPPPLSQEELTRSPCLKAVET 710
T LM LA GK+ LEGGY L S+ +S V+ LLGD P LS E +PC A+E+
Sbjct: 269 THLLMVLAGGKLCAVLEGGYHLESLAESVCMTVQTLLGDPLPRLSGE---MTPCQSALES 325
Query: 711 LQKTIAIQVSHW 722
+Q A Q +W
Sbjct: 326 IQNVRAAQAPYW 337
Score = 32.9 bits (75), Expect = 0.59
Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 465 LFDAEHEKKRKEQLKRLFERTPEQCGTGAGLGFNINIAWSGALNPPMGDAEYLSS 519
L+ + H + + L E + G G GLGFNIN+ W+ MG+A+YL++
Sbjct: 173 LYFSWHRYEHQRFWPFLRESDYDAVGRGKGLGFNINLPWNKV---GMGNADYLAA 224
>gnl|CDD|223201 COG0123, AcuC, Deacetylases, including yeast histone deacetylase
and acetoin utilization protein [Chromatin structure and
dynamics / Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 340
Score = 168 bits (428), Expect = 2e-46
Identities = 72/165 (43%), Positives = 93/165 (56%), Gaps = 11/165 (6%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGAL 592
+DVHHGNGTQ+IFY D VL +S+H+ D F+PGTGG E G G G N+NI
Sbjct: 161 FDVHHGNGTQEIFYDDDDVLTVSLHQ-DGRPFYPGTGGADEIGEG-KEGNNVNIPLP--- 215
Query: 593 NPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQ 652
P GD YL A IV+P+ +EF P +V+VSAGFDA G PLG L+ + + +
Sbjct: 216 -PGTGDDSYLEALEEIVLPLLEEFKPDLVIVSAGFDAHRGD--PLGRLNLTEEGYAKIGR 272
Query: 653 QLMTLA---DGKVVLALEGGYDLPSMCDSAEACVRALLGDAPPPL 694
+ LA G VV LEGGY+L ++ S A + L G L
Sbjct: 273 AVRKLAEGYGGPVVAVLEGGYNLDALARSLVAFLAGLAGLVEEEL 317
>gnl|CDD|212521 cd09996, HDAC_classII_1, Histone deacetylases and histone-like
deacetylases, classII. This subfamily includes
bacterial as well as eukaryotic Class II histone
deacetylase (HDAC) and related proteins. Deacetylases of
class II are Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine residues of histones
(EC 3.5.1.98) and possibly other proteins to yield
deacetylated histones/other proteins. Included in this
family is a bacterial HDAC-like amidohydrolase
(Bordetella/Alcaligenes species FB18817, denoted as
FB188 HDAH) shown to be most similar in sequence and
function to class II HDAC6 domain 3 or b (HDAC6b). FB188
HDAH is able to remove the acetyl moiety from acetylated
histones, and can be inhibited by common HDAC inhibitors
such as SAHA (suberoylanilide hydroxamic acid) as well
as class II-specific but not class I specific
inhibitors.
Length = 359
Score = 168 bits (429), Expect = 3e-46
Identities = 66/142 (46%), Positives = 88/142 (61%), Gaps = 12/142 (8%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGAL 592
WDVHHGNGTQ IFY D VL +S+H+ D F P +G E G GAG G+N+NI L
Sbjct: 174 WDVHHGNGTQAIFYDDPDVLTISLHQ--DRCFPPDSGAVEERGEGAGEGYNLNI----PL 227
Query: 593 NPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQ 652
P GD YL AF IV+P + F P++++V++GFDA+A PLG L+ F +T+
Sbjct: 228 PPGSGDGAYLHAFERIVLPALRAFRPELIIVASGFDASAFD--PLGRMMLTSDGFRALTR 285
Query: 653 QLMTLAD----GKVVLALEGGY 670
+L LAD G++V+ EGGY
Sbjct: 286 KLRDLADELCGGRLVMVHEGGY 307
Score = 35.6 bits (83), Expect = 0.099
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 487 EQCGTGAGLGFNINIAWSGALNPPMGDAEYL 517
E+ G GAG G+N+NI L P GD YL
Sbjct: 211 EERGEGAGEGYNLNI----PLPPGSGDGAYL 237
>gnl|CDD|212512 cd09301, HDAC, Histone deacetylase (HDAC) classes I, II, IV and
related proteins. The HDAC/HDAC-like family includes
Zn-dependent histone deacetylase classes I, II and IV
(class III HDACs, also called sirtuins, are
NAD-dependent and structurally unrelated, and therefore
not part of this family). Histone deacetylases catalyze
hydrolysis of N(6)-acetyl-lysine residues in histone
amino termini to yield a deacetylated histone (EC
3.5.1.98), as opposed to the acetylation reaction by
some histone acetyltransferases (EC 2.3.1.48).
Deacetylases of this family are involved in signal
transduction through histone and other protein
modification, and can repress/activate transcription of
a number of different genes. They usually act via the
formation of large multiprotein complexes. They are
involved in various cellular processes, including cell
cycle regulation, DNA damage response, embryonic
development, cytokine signaling important for immune
response and post-translational control of the acetyl
coenzyme A synthetase. In mammals, they are known to be
involved in progression of different tumors. Specific
inhibitors of mammalian histone deacetylases are an
emerging class of promising novel anticancer drugs.
Length = 279
Score = 151 bits (384), Expect = 4e-41
Identities = 50/155 (32%), Positives = 78/155 (50%), Gaps = 17/155 (10%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGAL 592
D HHG+GT++ FY D RVL++S H +D F G G G G+ IN+
Sbjct: 141 TDAHHGDGTREAFYDDDRVLHMSFHNYDIYPF----------GRGKGKGYKINVPLEDG- 189
Query: 593 NPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQ 652
+GD EYL A ++ V +EF+P++V++ G D G LGG+ LS F + +
Sbjct: 190 ---LGDEEYLDAVERVISKVLEEFEPEVVVLQFGHDTHEGD--RLGGFNLSEKGFVKLAE 244
Query: 653 QLMTLADGK-VVLALEGGYDLPSMCDSAEACVRAL 686
+ A G +++ L GGY+ + A ++ L
Sbjct: 245 IVKEFARGGPILMVLGGGYNPEAAARIWTAIIKEL 279
>gnl|CDD|212541 cd11599, HDAC_classII_2, Histone deacetylases and histone-like
deacetylases, classII. This subfamily includes
eukaryotic as well as bacterial Class II histone
deacetylase (HDAC) and related proteins. Deacetylases of
class II are Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine residues of histones
(EC 3.5.1.98) and possibly other proteins to yield
deacetylated histones/other proteins. In D. discoideum,
where four homologs (HdaA, HdaB, HdaC, HdaD) have been
identified, HDAC activity is important for regulating
the timing of gene expression during development. Also,
inhibition of HDAC activity by trichostatin A is shown
to cause hyperacetylation of the histone and a delay in
cell aggregation and differentiation.
Length = 288
Score = 150 bits (381), Expect = 1e-40
Identities = 68/163 (41%), Positives = 91/163 (55%), Gaps = 25/163 (15%)
Query: 533 WDVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGAL 592
+DVHHGNGT+ IF D RVL+ S H+H +PGTG P E TG G NI +
Sbjct: 143 FDVHHGNGTEDIFRDDPRVLFCSSHQH---PLYPGTGAPDE--TGHG---NI-------V 187
Query: 593 NPPM----GDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFG 648
N P+ G AE+ A +P F P ++L+SAGFDA PL L+ +
Sbjct: 188 NVPLPAGTGGAEFREAVEDRWLPALDAFKPDLILISAGFDAHRDD--PLAQLNLTEEDYA 245
Query: 649 YMTQQLMTLAD----GKVVLALEGGYDLPSMCDSAEACVRALL 687
++T+QLM +AD G++V LEGGYDL ++ S A VRAL+
Sbjct: 246 WITEQLMDVADRYCDGRIVSVLEGGYDLSALARSVAAHVRALM 288
>gnl|CDD|218611 pfam05499, DMAP1, DNA methyltransferase 1-associated protein 1
(DMAP1). DNA methylation can contribute to
transcriptional silencing through several
transcriptionally repressive complexes, which include
methyl-CpG binding domain proteins (MBDs) and histone
deacetylases (HDACs). The chief enzyme that maintains
mammalian DNA methylation, DNMT1, can also establish a
repressive transcription complex. The non-catalytic
amino terminus of DNMT1 binds to HDAC2 and DMAP1 (for
DNMT1 associated protein), and can mediate
transcriptional repression. DMAP1 has intrinsic
transcription repressive activity, and binds to the
transcriptional co-repressor TSG101. DMAP1 is targeted
to replication foci through interaction with the far N
terminus of DNMT1 throughout S phase, whereas HDAC2
joins DNMT1 and DMAP1 only during late S phase,
providing a platform for how histones may become
deacetylated in heterochromatin following replication.
Length = 175
Score = 143 bits (362), Expect = 2e-39
Identities = 77/176 (43%), Positives = 100/176 (56%), Gaps = 44/176 (25%)
Query: 239 EEQMLLAELKKIEIRRKERDRKTQDLQKLMTAADMQ------ADNRKTDKKMPPKRKLTH 292
EE+ L+AEL+KIE R+KER++K QDLQKL+TAAD Q A+ RK +KK+P K+K+
Sbjct: 1 EEEYLIAELRKIEARKKEREKKAQDLQKLITAADQQAAGFSTAEARKREKKLP-KKKIPQ 59
Query: 293 QIRPRSLDTSVKTTAF-----------------------------------QTLIDLG-- 315
+ P D+ V Q L +L
Sbjct: 60 KPGPSKEDSKVNVPETAGIKFPDFKSAGVSLRSQRMKLPANVGQKKIKALEQALEELKVD 119
Query: 316 LNPIPTEEIVTHYNELRSDMVLLYELKQALDNYQFELQSLKHQYEAVHPGETFQIP 371
LNP+PTEEI +NELRSDMVLLYELKQAL +FEL+SL+H+YEA+ PG+ IP
Sbjct: 120 LNPMPTEEICQMFNELRSDMVLLYELKQALGTCEFELESLRHRYEALAPGKDLNIP 175
>gnl|CDD|212525 cd10001, HDAC_classII_APAH, Histone deacetylase class IIa. This
subfamily includes bacterial acetylpolyamine
amidohydrolase (APAH) as well as other Class II histone
deacetylase (HDAC) and related proteins. Deacetylases of
class II are Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine residues of histones
(EC 3.5.1.98) and possibly other proteins to yield
deacetylated histones/other proteins. Mycoplana ramosa
APAH exhibits broad substrate specificity and catalyzes
the deacetylation of polyamines such as putrescine,
spermidine, and spermine by cleavage of a non-peptide
amide bond.
Length = 298
Score = 146 bits (371), Expect = 4e-39
Identities = 58/156 (37%), Positives = 80/156 (51%), Gaps = 14/156 (8%)
Query: 534 DVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGG-PIECGTGAGLGFNINIAWSGAL 592
DVHHGNGTQ+IFY VLY+SIH D F+P G E G G G G+N+N+ L
Sbjct: 153 DVHHGNGTQEIFYERPDVLYVSIHG-DPRTFYPFFLGFADETGEGEGEGYNLNL----PL 207
Query: 593 NPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQ 652
P GD +YLAA + +A F P ++VS GFD G PL +KL+ + + +
Sbjct: 208 PPGTGDDDYLAALDEALAAIA-AFGPDALVVSLGFDTHEGD--PLSDFKLTTEDYARIGR 264
Query: 653 QLMTLADGKVVLALEGGYDLPSMCDSAEACVRALLG 688
++ L V EGGY++ ++ A L
Sbjct: 265 RIAAL-GLPTVFVQEGGYNVDAL----GRNAVAFLA 295
Score = 32.1 bits (74), Expect = 1.1
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 4/32 (12%)
Query: 486 PEQCGTGAGLGFNINIAWSGALNPPMGDAEYL 517
++ G G G G+N+N+ L P GD +YL
Sbjct: 190 ADETGEGEGEGYNLNL----PLPPGTGDDDYL 217
>gnl|CDD|212520 cd09994, HDAC_AcuC_like, Class I histone deacetylase AcuC (Acetoin
utilization protein)-like enzymes. AcuC (Acetoin
utilization protein) is a class I deacetylase found only
in bacteria and is involved in post-translational
control of the acetyl-coenzyme A synthetase (AcsA).
Deacetylase AcuC works in coordination with deacetylase
SrtN (class III), possibly to maintain AcsA in active
(deacetylated) form and let the cell grow under low
concentration of acetate. B. subtilis AcuC is a member
of operon acuABC; this operon is repressed by the
presence of glucose and does not show induction by
acetoin; acetoin is a bacterial fermentation product
that can be converted to acetate via the butanediol
cycle in absence of other carbon sources. Inactivation
of AcuC leads to slower growth and lower cell yield
under low-acetate conditions in Bacillus subtilis. In
general, Class I histone deacetylases (HDACs) are
Zn-dependent enzymes that catalyze hydrolysis of
N(6)-acetyl-lysine residues in histone amino termini to
yield a deacetylated histone (EC 3.5.1.98). Enzymes
belonging to this group participate in regulation of a
number of processes through protein (mostly different
histones) modification (deacetylation). Class I histone
deacetylases in general act via the formation of large
multiprotein complexes. Members of this class are
involved in cell cycle regulation, DNA damage response,
embryonic development, cytokine signaling important for
immune response and in posttranslational control of the
acetyl coenzyme A synthetase.
Length = 313
Score = 121 bits (306), Expect = 3e-30
Identities = 54/143 (37%), Positives = 73/143 (51%), Gaps = 11/143 (7%)
Query: 534 DVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGALN 593
D HHG+G Q FY D RVL +S+H FPGTG E G G G G+ +NI L
Sbjct: 164 DAHHGDGVQAAFYDDPRVLTISLHE-SGRYLFPGTGFVDEIGEGEGYGYAVNI----PLP 218
Query: 594 PPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQQ 653
P GD E+L AF +V P+ + F P +++ G DA AG PL LS + ++
Sbjct: 219 PGTGDDEFLRAFEAVVPPLLRAFRPDVIVSQHGADAHAGD--PLTHLNLSNRAYRAAVRR 276
Query: 654 LMTLAD----GKVVLALEGGYDL 672
+ LAD G+ + GGY+
Sbjct: 277 IRELADEYCGGRWLALGGGGYNP 299
Score = 29.5 bits (67), Expect = 7.4
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 6/41 (14%)
Query: 479 KRLFERT--PEQCGTGAGLGFNINIAWSGALNPPMGDAEYL 517
+ LF T ++ G G G G+ +NI L P GD E+L
Sbjct: 191 RYLFPGTGFVDEIGEGEGYGYAVNI----PLPPGTGDDEFL 227
>gnl|CDD|212517 cd09991, HDAC_classI, Class I histone deacetylases. Class I
histone deacetylases (HDACs) are Zn-dependent enzymes
that catalyze hydrolysis of N(6)-acetyl-lysine residues
in histone amino termini to yield a deacetylated histone
(EC 3.5.1.98). Enzymes belonging to this group
participate in regulation of a number of processes
through protein (mostly different histones) modification
(deacetylation). Class I histone deacetylases in general
act via the formation of large multiprotein complexes.
This group includes animal HDAC1, HDAC2, HDAC3, HDAC8,
fungal RPD3, HOS1 and HOS2, plant HDA9, protist,
archaeal and bacterial (AcuC) deacetylases. Members of
this class are involved in cell cycle regulation, DNA
damage response, embryonic development, cytokine
signaling important for immune response and in
posttranslational control of the acetyl coenzyme A
synthetase. In mammals, they are known to be involved in
progression of various tumors. Specific inhibitors of
mammalian histone deacetylases are an emerging class of
promising novel anticancer drugs.
Length = 306
Score = 98.0 bits (245), Expect = 3e-22
Identities = 36/123 (29%), Positives = 59/123 (47%), Gaps = 12/123 (9%)
Query: 534 DVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGALN 593
D+HHG+G ++ FY+ RV+ +S H+ G +F G + G G G + +N+ L
Sbjct: 163 DIHHGDGVEEAFYTTDRVMTVSFHKF--GEYFFPGTGLRDIGAGKGKYYAVNV----PLK 216
Query: 594 PPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSP----ACFGY 649
+ D YL F ++ V + F P V++ G D+ AG LG + LS C +
Sbjct: 217 DGIDDESYLQIFEPVLSKVMEVFQPSAVVLQCGADSLAGD--RLGCFNLSIKGHAKCVKF 274
Query: 650 MTQ 652
+
Sbjct: 275 VKS 277
>gnl|CDD|212543 cd11680, HDAC_Hos1, Class I histone deacetylases Hos1 and related
proteins. Saccharomyces cerevisiae Hos1 is responsible
for Smc3 deacetylation. Smc3 is an important player
during the establishment of sister chromatid cohesion.
Hos1 belongs to the class I histone deacetylases
(HDACs). HDACs are Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine residues in histone
amino termini to yield a deacetylated histone (EC
3.5.1.98). Enzymes belonging to this group participate
in regulation of a number of processes through protein
(mostly different histones) modification
(deacetylation). Class I histone deacetylases in general
act via the formation of large multiprotein complexes.
Other class I HDACs are animal HDAC1, HDAC2, HDAC3,
HDAC8, fungal RPD3 and HOS2, plant HDA9, protist,
archaeal and bacterial (AcuC) deacetylases. Members of
this class are involved in cell cycle regulation, DNA
damage response, embryonic development, cytokine
signaling important for immune response and in
posttranslational control of the acetyl coenzyme A
synthetase.
Length = 294
Score = 89.6 bits (223), Expect = 1e-19
Identities = 43/136 (31%), Positives = 67/136 (49%), Gaps = 11/136 (8%)
Query: 534 DVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGALN 593
D+HHG+G + F+ K VL SIHR+D G FFPGTG +NI L
Sbjct: 152 DLHHGDGVESAFFFSKNVLTCSIHRYDPG-FFPGTGSLKNSSD----KGMLNI----PLK 202
Query: 594 PPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQQ 653
+ D L +IV P+ ++F+P+++++ G D +G P + L+ +G + +
Sbjct: 203 RGLSDKTLLRIIDSIVRPLIEKFEPEVIVIQCGCDGLSGD--PHKEWNLTIRGYGSVIEL 260
Query: 654 LMTLADGKVVLALEGG 669
L+ K L L GG
Sbjct: 261 LLKEFKDKPTLLLGGG 276
>gnl|CDD|212556 cd11658, SANT_DMAP1_like, SANT/myb-like domain of Human Dna
Methyltransferase 1 Associated Protein 1-like. These
proteins are members of the SANT/myb group. SANT is
named after 'SWI3, ADA2, N-CoR and TFIIIB', several
factors that share this domain. The SANT domain
resembles the 3 alpha-helix bundle of the DNA-binding
Myb domains and is found in a diverse set of proteins.
Length = 46
Score = 73.2 bits (180), Expect = 2e-16
Identities = 28/49 (57%), Positives = 36/49 (73%), Gaps = 3/49 (6%)
Query: 146 WTRAETDHLFDLCHRFDLRFIVIHDRYDTNKFPTSRTIEDLKQRYYFVC 194
WT+ ETD+LFDL RFDLR+ VI DRY K R++EDLK++YY +C
Sbjct: 1 WTKEETDYLFDLVKRFDLRWNVILDRYPFQK---GRSVEDLKEKYYHLC 46
Score = 73.2 bits (180), Expect = 2e-16
Identities = 28/49 (57%), Positives = 36/49 (73%), Gaps = 3/49 (6%)
Query: 398 WTRAETDHLFDLCHRFDLRFIVIHDRYDTNKFPTSRTIEDLKQRYYFVC 446
WT+ ETD+LFDL RFDLR+ VI DRY K R++EDLK++YY +C
Sbjct: 1 WTKEETDYLFDLVKRFDLRWNVILDRYPFQK---GRSVEDLKEKYYHLC 46
>gnl|CDD|212540 cd11598, HDAC_Hos2, Class I histone deacetylases including ScHos2
and SpPhd1. This subfamily includes Class I histone
deacetylase (HDAC) Hos2 from Saccharomyces cerevisiae as
well as a histone deacetylase Phd1 from
Schizosaccharomyces pombe. Hos2 binds to the coding
regions of genes during gene activation, specifically it
deacetylates the lysines in H3 and H4 histone tails. It
is preferentially associated with genes of high activity
genome-wide and is shown to be necessary for efficient
transcription. Thus, Hos2 is directly required for gene
activation in contrast to other class I histone
deacetylases. Protein encoded by phd1 is inhibited by
trichostatin A (TSA), a specific inhibitor of histone
deacetylase, and is involved in the meiotic cell cycle
in S. pombe. Class 1 HDACs are Zn-dependent enzymes that
catalyze hydrolysis of N(6)-acetyl-lysine residues in
histone amino termini to yield a deacetylated histone
(EC 3.5.1.98).
Length = 311
Score = 80.2 bits (198), Expect = 3e-16
Identities = 50/165 (30%), Positives = 79/165 (47%), Gaps = 25/165 (15%)
Query: 498 NINIAWSGALNPPMGDAEYLSSDG-----------REKTQYFPFRCW---DVHHGNGTQQ 543
+I I WSG L+ A+ + G +YFP + DVHHG+G ++
Sbjct: 121 DIAINWSGGLH----HAKKSEASGFCYVNDIVLAILNLLRYFPRVLYIDIDVHHGDGVEE 176
Query: 544 IFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGALNPPMGDAEYLA 603
FY RV+ LS H++ +G FFPGTG + G G F +N+ L + D +Y
Sbjct: 177 AFYRTDRVMTLSFHKY-NGEFFPGTGDLDDNGGTPGKHFALNV----PLEDGIDDEQYNL 231
Query: 604 AFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFG 648
F++I+ P ++F P +++ G D+ G LG + L+ G
Sbjct: 232 LFKSIIGPTIEKFQPSAIVLQCGADSLGGD--RLGQFNLNIKAHG 274
>gnl|CDD|212513 cd09987, Arginase_HDAC, Arginase-like and histone-like hydrolases.
Arginase-like/histone-like hydrolase superfamily
includes metal-dependent enzymes that belong to
Arginase-like amidino hydrolase family and
histone/histone-like deacetylase class I, II, IV family,
respectively. These enzymes catalyze hydrolysis of amide
bond. Arginases are known to be involved in control of
cellular levels of arginine and ornithine, in histidine
and arginine degradation and in clavulanic acid
biosynthesis. Deacetylases play a role in signal
transduction through histone and/or other protein
modification and can repress/activate transcription of a
number of different genes. They participate in different
cellular processes including cell cycle regulation, DNA
damage response, embryonic development, cytokine
signaling important for immune response and
post-translational control of the acetyl coenzyme A
synthetase. Mammalian histone deacetyases are known to
be involved in progression of different tumors. Specific
inhibitors of mammalian histone deacetylases are an
emerging class of promising novel anticancer drugs.
Length = 217
Score = 77.0 bits (190), Expect = 6e-16
Identities = 30/176 (17%), Positives = 43/176 (24%), Gaps = 37/176 (21%)
Query: 533 WDVHHGNGTQQIFY--------------SDKRVLYLSIHRHDDGNFFPGTGGPIECGTGA 578
D HH T + F V +SI N G G A
Sbjct: 57 VDAHHDVRTPEAFGKGNHHTPRHLLCEPLISDVHIVSIGIRGVSNGEAG-------GAYA 109
Query: 579 GLGFNINIAWSGALNPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPP-- 636
+ + + + F IV + V +S D P
Sbjct: 110 RKLGVVYFSMTE-----VDKLGLGDVFEEIVSYL--GDKGDNVYLSVDVDGLDPSFAPGT 162
Query: 637 --LGGYKLSPACFGYMTQQLMTLADGKVVLALEGGYDLPSM----CDSAEACVRAL 686
G LS Y+T+++ V L + L A A L
Sbjct: 163 GTPGPGGLSYREGLYITERIAKTN-LVVGLDIVEVNPLLDETGRTARLAAALTLEL 217
>gnl|CDD|212524 cd10000, HDAC8, Histone deacetylase 8 (HDAC8). HDAC8 is a
Zn-dependent class I histone deacetylase that catalyzes
hydrolysis of an N(6)-acetyl-lysine residue of a histone
to yield a deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. HDAC8 is found in human cytoskeleton-bound
protein fraction and insoluble cell pellets. It plays a
crucial role in intramembraneous bone formation;
germline deletion of HDAC8 is detrimental to skull bone
formation. HDAC8 is possibly associated with the smooth
muscle actin cytockeleton and may regulate the
contractive capacity of smooth muscle cells. HDAC8 is
also involved in the metabolic control of the estrogen
receptor related receptor (ERR)-alpha/peroxisome
proliferator activated receptor (PPAR) gamma coactivator
1 alpha (PGC1-alpha) transcriptional complex as well as
in the development of neuroblastoma and T-cell lymphoma.
HDAC8-selective small-molecule inhibitors could be a
therapeutic drug option for these diseases.
Length = 364
Score = 75.8 bits (187), Expect = 1e-14
Identities = 44/142 (30%), Positives = 71/142 (50%), Gaps = 10/142 (7%)
Query: 534 DVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGALN 593
D+HHG+G + F +V+ +S+H++ G FFPGTG + G G G + +N+ +
Sbjct: 165 DLHHGDGVEDAFSFTSKVMTVSLHKYSPG-FFPGTGDVSDVGLGKGKYYTVNVPLRDGIQ 223
Query: 594 PPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQQ 653
D +YL F +V + F P+ V++ G D AG P+G + L+P G +
Sbjct: 224 ----DEQYLQIFTAVVPEIVAAFRPEAVVLQCGADTLAGD--PMGAFNLTPVGIGKCLKY 277
Query: 654 LMTLADGKVVLAL-EGGYDLPS 674
+ L L L GGY+L +
Sbjct: 278 V--LGWKLPTLILGGGGYNLAN 297
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 72.8 bits (178), Expect = 2e-13
Identities = 47/137 (34%), Positives = 71/137 (51%), Gaps = 11/137 (8%)
Query: 534 DVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIA-WSGAL 592
D+HHG+G + F + RV LS+H+ + +FFPGTG P + G G G +++N+A W G
Sbjct: 190 DMHHGDGVDEAFCTSDRVFTLSLHKFGE-SFFPGTGHPRDVGYGRGRYYSMNLAVWDG-- 246
Query: 593 NPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPACFGYMTQ 652
+ D YL F + + + + P +++ G D+ AG LG LS G Q
Sbjct: 247 ---ITDFYYLGLFEHALHSIVRRYSPDAIVLQCGADSLAGD--RLGLLNLSSFGHGQCVQ 301
Query: 653 QLMTLADGKVVLALEGG 669
+ L G +LAL GG
Sbjct: 302 AVRDL--GIPMLALGGG 316
>gnl|CDD|212528 cd10004, RPD3-like, reduced potassium dependency-3 (RPD3)-like.
Proteins of the Rpd3-like family are class I
Zn-dependent Histone deacetylases that catalyze
hydrolysis of an N(6)-acetyl-lysine residue of a histone
to yield a deacetylated histone (EC 3.5.1.98). RPD3 is
the yeast homolog of class I HDACs. The main function of
RPD3-like group members is regulation of a number of
different processes through protein (mostly different
histones) modification (deacetylation). This group
includes fungal RPD3 and acts via the formation of large
multiprotein complexes. Members of this group are
involved in cell cycle regulation, DNA damage response,
embryonic development and cytokine signaling important
for immune response. Histone deacetylation by yeast RPD3
represses genes regulated by the Ash1 and Ume6
DNA-binding proteins. In mammals, they are known to be
involved in progression of various tumors. Specific
inhibitors of mammalian histone deacetylases could be a
therapeutic drug option.
Length = 375
Score = 72.1 bits (177), Expect = 3e-13
Identities = 36/110 (32%), Positives = 60/110 (54%), Gaps = 8/110 (7%)
Query: 534 DVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGALN 593
DVHHG+G ++ FY+ RV+ S H++ G +FPGTG + G G G + +N+ L
Sbjct: 169 DVHHGDGVEEAFYTTDRVMTCSFHKY--GEYFPGTGELRDIGIGTGKNYAVNV----PLR 222
Query: 594 PPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLS 643
+ D Y + F ++ V + + P+ V++ G D+ +G LG + LS
Sbjct: 223 DGIDDESYKSIFEPVIKHVMEWYQPEAVVLQCGGDSLSGD--RLGCFNLS 270
>gnl|CDD|212519 cd09993, HDAC_classIV, Histone deacetylase class IV also known as
histone deacetylase 11. Class IV histone deacetylases
(HDAC11; EC 3.5.1.98) are predicted Zn-dependent
enzymes. This class includes animal HDAC11, plant HDA2
and related bacterial deacetylases. Enzymes in this
subfamily participate in regulation of a number of
different processes through protein modification
(deacetylation). They catalyze hydrolysis of
N(6)-acetyl-lysine of histones (or other proteins) to
yield a deacetylated proteins. Histone deacetylases
often act as members of large multi-protein complexes
such as mSin3A or SMRT/N-CoR. Human HDAC11 does not
associate with them but can interact with HDAC6 in vivo.
It has been suggested that HDAC11 and HDAC6 may use
non-histone proteins as their substrates and play a role
other than to directly modulate chromatin structure. In
normal tissues, expression of HDAC11 is limited to
kidney, heart, brain, skeletal muscle and testis,
suggesting that its function might be tissue-specific.
In mammals, HDAC11 proteins are known to be involved in
progression of various tumors. HDAC11 plays an essential
role in regulating OX40 ligand (OX40L) expression in
Hodgkin lymphoma (HL); selective inhibition of HDAC11
expression significantly up-regulates OX40L and induces
apoptosis in HL cell lines. Thus, inhibition of HDAC11
could be a therapeutic drug option for antitumor immune
response in HL patients.
Length = 275
Score = 67.5 bits (166), Expect = 2e-12
Identities = 36/112 (32%), Positives = 46/112 (41%), Gaps = 19/112 (16%)
Query: 534 DVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGALN 593
DVH GNGT IF D V S+H +P P ++++ L
Sbjct: 140 DVHQGNGTAAIFADDPSVFTFSMH---GEKNYPFRKEPS----------DLDV----PLP 182
Query: 594 PPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLSPA 645
GD EYLAA + + EF P +V +AG D AG LG LS
Sbjct: 183 DGTGDDEYLAALEEALPRLLAEFRPDLVFYNAGVDVLAGD--RLGRLSLSLE 232
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 69.1 bits (169), Expect = 3e-12
Identities = 33/110 (30%), Positives = 59/110 (53%), Gaps = 8/110 (7%)
Query: 534 DVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGALN 593
DVHHG+G ++ FY RV+ +S H+ G+FFPGTG + G G +++N+ LN
Sbjct: 173 DVHHGDGVEEAFYVTHRVMTVSFHKF--GDFFPGTGDVTDIGVAQGKYYSVNV----PLN 226
Query: 594 PPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLS 643
+ D ++ F+ ++ + + P +++ G D+ G LG + L+
Sbjct: 227 DGIDDDSFVDLFKPVISKCVEVYRPGAIVLQCGADSLTGD--RLGRFNLT 274
>gnl|CDD|212529 cd10005, HDAC3, Histone deacetylase 3 (HDAC3). HDAC3 is a
Zn-dependent class I histone deacetylase that catalyzes
hydrolysis of N(6)-acetyl-lysine residue of a histone to
yield a deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
In order to target specific chromatin regions, HDAC3 can
interact with DNA-binding proteins (transcriptional
factors) either directly or after forming complexes with
a number of other proteins, as observed for the
SMPT/N-CoR complex which recruits human HDAC3 to
specific chromatin loci and activates deacetylation.
Human HDAC3 is also involved in deacetylation of
non-histone substrates such as RelA, SPY and p53
factors. This protein can also down-regulate p53
function and subsequently modulate cell growth and
apoptosis. This gene is therefore regarded as a
potential tumor suppressor gene. HDAC3 plays a role in
various physiological processes, including subcellular
protein localization, cell cycle progression, cell
differentiation, apoptosis and survival. HDAC3 has been
found to be overexpressed in some tumors including
leukemia, lung carcinoma, colon cancer and maxillary
carcinoma. Thus, inhibitors precisely targeting HDAC3
(in some cases together with retinoic acid or
hyperthermia) could be a therapeutic drug option.
Length = 381
Score = 68.2 bits (167), Expect = 4e-12
Identities = 37/111 (33%), Positives = 59/111 (53%), Gaps = 9/111 (8%)
Query: 534 DVHHGNGTQQIFYSDKRVLYLSIHRHDDGN-FFPGTGGPIECGTGAGLGFNINIAWSGAL 592
D+HHG+G Q+ FY RV+ +S H++ GN FFPGTG E G +G +++N+ L
Sbjct: 168 DIHHGDGVQEAFYLTDRVMTVSFHKY--GNYFFPGTGDMYEVGAESGRYYSVNV----PL 221
Query: 593 NPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGYKLS 643
+ D YL F+ ++ V + P +++ G D+ LG + LS
Sbjct: 222 KDGIDDQSYLQLFKPVIQQVIDFYQPTCIVLQCGADSLGCD--RLGCFNLS 270
>gnl|CDD|212534 cd10010, HDAC1, Histone deacetylase 1 (HDAC1). Histone deacetylase
1 (HDAC1) is a Zn-dependent class I enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDAC1 is involved in regulation through
association with DNA binding proteins to target specific
chromatin regions. In particular, HDAC1 appears to play
a major role in pre-implantation embryogenesis in
establishing a repressive chromatin state. Its
interaction with retinoblastoma tumor-suppressor protein
is essential in the control of cell proliferation and
differentiation. Together with metastasis-associated
protein-2 (MTA2), it deacetylates p53, thereby
modulating its effect on cell growth and apoptosis. It
participates in DNA-damage response, along with HDAC2;
together, they promote DNA non-homologous end-joining.
HDAC1 is also involved in tumorogenesis; its
overexpression modulates cancer progression. Specific
inhibitors of HDAC1 are currently used in cancer
therapy.
Length = 371
Score = 66.6 bits (162), Expect = 1e-11
Identities = 33/99 (33%), Positives = 55/99 (55%), Gaps = 6/99 (6%)
Query: 534 DVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGALN 593
D+HHG+G ++ FY+ RV+ +S H++ G +FPGTG + G G G + +N L
Sbjct: 173 DIHHGDGVEEAFYTTDRVMTVSFHKY--GEYFPGTGDLRDIGAGKGKYYAVNY----PLR 226
Query: 594 PPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAG 632
+ D Y A F+ ++ V + F P V++ G D+ +G
Sbjct: 227 DGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGADSLSG 265
>gnl|CDD|212535 cd10011, HDAC2, Histone deacetylase 2 (HDAC2). Histone deacetylase
2 (HDAC2) is a Zn-dependent class I enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDAC2 is involved in regulation through
association with DNA binding proteins to target specific
chromatin regions. It forms transcriptional repressor
complexes by associating with several proteins,
including the mammalian zinc-finger transcription factor
YY1, thus playing an important role in transcriptional
regulation, cell cycle progression and developmental
events. Additionally, a few non-histone HDAC2 substrates
have been found. HDAC2 plays a role in embryonic
development and cytokine signaling important for immune
response, and is over-expressed in several solid tumors
including oral, prostate, ovarian, endometrial and
gastric cancer. It participates in DNA-damage response,
along with HDAC1; together, they can promote DNA
non-homologous end-joining. HDAC2 is considered an
important cancer prognostic marker. Inhibitors
specifically targeting HDAC2 could be a therapeutic drug
option.
Length = 366
Score = 53.9 bits (129), Expect = 2e-07
Identities = 31/99 (31%), Positives = 52/99 (52%), Gaps = 6/99 (6%)
Query: 534 DVHHGNGTQQIFYSDKRVLYLSIHRHDDGNFFPGTGGPIECGTGAGLGFNINIAWSGALN 593
D+HHG+G ++ FY+ RV+ +S H G +FPGTG + G G G + +N ++
Sbjct: 169 DIHHGDGVEEAFYTTDRVMTVS--FHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGID 226
Query: 594 PPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAG 632
D Y F+ I+ V + + P V++ G D+ +G
Sbjct: 227 ----DESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSG 261
>gnl|CDD|212522 cd09998, HDAC_Hos3, Class II histone deacetylases Hos3 and related
proteins. Fungal histone deacetylase Hos3 from
Saccharomyces cerevisiae is a Zn-dependent enzyme
belonging to HDAC class II. It catalyzes hydrolysis of
an N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. Hos3 deacetylase is homodimer, in vitro it
shows specificity to H4, H3 and H2A.
Length = 353
Score = 44.0 bits (104), Expect = 2e-04
Identities = 53/202 (26%), Positives = 77/202 (38%), Gaps = 56/202 (27%)
Query: 534 DVHHGNGTQQI----------------FYSDK--------RVLYLSIHRHDDGNFFPGTG 569
D+HHGNGTQ I Y D R+ Y S+H D N FP
Sbjct: 158 DLHHGNGTQDIAWRINAEANKQALESSSYDDFKPAGAPGLRIFYSSLH---DINSFPCED 214
Query: 570 GPIE-------CGTGAGLGFNINIAWSGALNPPMGDAEYLAAFR---TIVMPVAKEF--- 616
G GA G I W+ L P + ++ + I+ A EF
Sbjct: 215 GDPAKVKDASVSIDGA-HGQWI---WNVHLQPWTTEEDFWELYYPKYRILFEKAAEFLRL 270
Query: 617 ----DPQ--IVLVSAGFDAAAGHPPPLGGYKLS-PACFGY-MTQQLMTLAD----GKVVL 664
P +V +SAGFDA+ + + ++ P F Y + + AD G+++
Sbjct: 271 TTAATPFKTLVFISAGFDASEHEYESMQRHGVNVPTSFYYRFARDAVRFADAHAHGRLIS 330
Query: 665 ALEGGYDLPSMCDSAEACVRAL 686
LEGGY ++C A + L
Sbjct: 331 VLEGGYSDRALCSGVLAHLTGL 352
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 34.3 bits (79), Expect = 0.17
Identities = 17/87 (19%), Positives = 36/87 (41%), Gaps = 8/87 (9%)
Query: 219 EKKRKEQLKRLFERTPEQVEEEQMLLAELKKIE--------IRRKERDRKTQDLQKLMTA 270
+ +R+++L++L E +Q E++ AEL++ R+K + Q K
Sbjct: 97 QAQRQKKLQKLLEEKQKQEREKEREEAELRQRLAKEKYEEWCRQKAQQAAKQRTPKHKKE 156
Query: 271 ADMQADNRKTDKKMPPKRKLTHQIRPR 297
A A + + P + + + R
Sbjct: 157 AAESASSSLSGSAKPERNVSQEEAKKR 183
>gnl|CDD|234352 TIGR03779, Bac_Flav_CT_M, Bacteroides conjugative transposon TraM
protein. Members of this protein family are designated
TraM and are found in a proposed transfer region of a
class of conjugative transposon found in the Bacteroides
lineage [Cellular processes, DNA transformation].
Length = 410
Score = 34.3 bits (79), Expect = 0.27
Identities = 17/80 (21%), Positives = 28/80 (35%), Gaps = 9/80 (11%)
Query: 209 NEPKLFDAEHEKKRKEQLKRLFERTPEQVEEEQMLLAELKKI-EIRRKERDRKTQDLQKL 267
PK + + + E+L+ P E + LA ++K E+ K R + L
Sbjct: 138 EYPKTDEEKELLREVEELESRLATEPSPAPELEEQLALMEKSYELAAKYMPRGQERLP-- 195
Query: 268 MTAADMQADNRKTDKKMPPK 287
A K KK +
Sbjct: 196 ------VAPESKKGKKPSVQ 209
>gnl|CDD|218215 pfam04696, Pinin_SDK_memA, pinin/SDK/memA/ protein conserved
region. Members of this family have very varied
localisations within the eukaryotic cell. pinin is known
to localise at the desmosomes and is implicated in
anchoring intermediate filaments to the desmosomal
plaque. SDK2/3 is a dynamically localised nuclear
protein thought to be involved in modulation of
alternative pre-mRNA splicing. memA is a tumour marker
preferentially expressed in human melanoma cell lines. A
common feature of the members of this family is that
they may all participate in regulating protein-protein
interactions.
Length = 131
Score = 32.1 bits (73), Expect = 0.42
Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 9/82 (10%)
Query: 217 EHEKKRKEQLKRLFERTPEQVEEEQMLLAELKKIEIRRKERDRKTQDLQKLMTAADMQAD 276
EK+R E ++L E+ ++ EE + EL E RR+++ + QK+ +
Sbjct: 32 SKEKRRAEIEQKLEEQEKQEREELRKEKREL--FEERRRKQLELRKLEQKMEDEKLQETW 89
Query: 277 NRKTDKKMPPKRKLTHQIRPRS 298
+ L + IR ++
Sbjct: 90 HEH-------NLALANFIRTKT 104
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 33.4 bits (76), Expect = 0.58
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 7/80 (8%)
Query: 216 AEHEKKRKEQLKRLFERTPEQVEEEQMLLAELKKIEIRRKERDRKTQDLQKLMTAADMQA 275
+ ++K+KE+LK+L E T E + E + L ELK E++ KE+ +K + +L +
Sbjct: 166 SREKRKKKERLKKLIEET-ENLAELIIDLEELKLQELKLKEQAKKALEYYQL------KE 218
Query: 276 DNRKTDKKMPPKRKLTHQIR 295
++ + L
Sbjct: 219 KLELEEENLLYLDYLKLNEE 238
>gnl|CDD|224234 COG1315, COG1315, Uncharacterized conserved protein [Function
unknown].
Length = 543
Score = 32.8 bits (75), Expect = 0.71
Identities = 19/76 (25%), Positives = 27/76 (35%), Gaps = 16/76 (21%)
Query: 234 PEQVEEEQMLLAELKKIEIRRKERDRKTQDLQKLMTAADMQADNRKTDKKMPPKRKLTHQ 293
PE VE + L E+ E + + L KL+ + K + K K L
Sbjct: 406 PEIVERLKELTEEISLHE-------ERLKKLTKLL----VALVKVKIESK---KNILP-- 449
Query: 294 IRPRSLDTSVKTTAFQ 309
SL T+V T
Sbjct: 450 PDKESLLTAVNNTKIT 465
>gnl|CDD|224292 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 398
Score = 32.4 bits (74), Expect = 0.95
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 304 KTTAFQTLIDLGLNP---IPTEEIVTHYNELRSDMVLLYELKQALDNYQF--ELQSLKHQ 358
KTT + LI L I +++ EL + ELK+ +Y F E+Q++
Sbjct: 50 KTTLLKLLIKGLLEEIIYINFDDLRLDRIELLDLLRAYIELKEREKSYIFLDEIQNVPDW 109
Query: 359 YEAV 362
A+
Sbjct: 110 ERAL 113
>gnl|CDD|222040 pfam13311, DUF4080, Protein of unknown function (DUF4080). A
family of uncharacterized proteins found by clustering
human gut metagenomic sequences.
Length = 187
Score = 31.4 bits (72), Expect = 1.1
Identities = 9/49 (18%), Positives = 23/49 (46%)
Query: 207 GGNEPKLFDAEHEKKRKEQLKRLFERTPEQVEEEQMLLAELKKIEIRRK 255
+ P+ DAE +K+ KE+++ + + E++ ++R+
Sbjct: 119 AKSRPEFLDAEDDKEEKEEIREFYLKEEEKLRYYLPEYEGTDAKQLRKM 167
>gnl|CDD|222961 PHA03005, PHA03005, sulfhydryl oxidase; Provisional.
Length = 96
Score = 29.6 bits (67), Expect = 1.5
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 6/33 (18%)
Query: 165 FIVIHDRYDTNKFPTSRTIEDLKQRYYFVCHTL 197
FIVI +K IE K++ Y +C TL
Sbjct: 15 FIVI------SKAKLDGNIEACKRKLYTICSTL 41
Score = 28.9 bits (65), Expect = 2.5
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 6/33 (18%)
Query: 417 FIVIHDRYDTNKFPTSRTIEDLKQRYYFVCYTL 449
FIVI +K IE K++ Y +C TL
Sbjct: 15 FIVI------SKAKLDGNIEACKRKLYTICSTL 41
>gnl|CDD|238285 cd00515, HAM1, NTPase/HAM1. This family consists of the HAM1
protein and pyrophosphate-releasing xanthosine/ inosine
triphosphatase. HAM1 protects the cell against
mutagenesis by the base analog 6-N-hydroxylaminopurine
(HAP) in E. Coli and S. cerevisiae. A Ham1-related
protein from Methanococcus jannaschii is a novel NTPase
that has been shown to hydrolyze nonstandard nucleotides
such as XTP to XMP and ITP to IMP, but not the standard
nucleotides, in the presence of Mg or Mn ions. The
enzyme exists as a homodimer. The HAM1 protein may be
acting as an NTPase by hydrolyzing the HAP triphosphate.
Length = 183
Score = 31.0 bits (71), Expect = 1.6
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 340 ELKQALDNYQFELQSLKHQYEAVHPGETF 368
E K+ L + E+ SLK + G TF
Sbjct: 13 EFKEILAPFGIEVVSLKDIIDIEETGSTF 41
>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain. This is a family of proteins of
approximately 300 residues, found in plants and
vertebrates. They contain a highly conserved DDRGK
motif.
Length = 189
Score = 30.8 bits (70), Expect = 1.9
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 215 DAEHEKKRKEQLKRLFERTPEQVEEEQMLLAELKKIEIRRKERDRKTQDLQK 266
+ E E+++K + KR ER E+ EE+ E KK E RKER+ + + Q+
Sbjct: 25 EEEREERKKLEEKREGERKEEEELEEE---REKKKEEEERKEREEQARKEQE 73
>gnl|CDD|240416 PTZ00432, PTZ00432, falcilysin; Provisional.
Length = 1119
Score = 31.7 bits (72), Expect = 1.9
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 208 GNEPKLFDAEHEKKRKEQLK-RLFERTPEQVEEEQMLLAELKKIEIRRKERDRKTQDLQK 266
E ++ E K K++LK RL T EQV+E + + KK R + D + D
Sbjct: 573 AVESSKYEKEFNKLVKDELKERLSHLTKEQVDEMEKAYEKFKK--EREADDDPEHLDSFP 630
Query: 267 LMTAADMQADN 277
+++ +D+ +
Sbjct: 631 ILSLSDLNKET 641
>gnl|CDD|217933 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an
obligate intracellular bacterium that develops within a
parasitophorous vacuole termed an inclusion. The
inclusion is non-fusogenic with lysosomes but intercepts
lipids from a host cell exocytic pathway. Initiation of
chlamydial development is concurrent with modification
of the inclusion membrane by a set of C.
trachomatis-encoded proteins collectively designated
Incs. One of these Incs, IncA, is functionally
associated with the homotypic fusion of inclusions. This
family probably includes members of the wider Inc family
rather than just IncA.
Length = 186
Score = 30.1 bits (68), Expect = 2.6
Identities = 35/139 (25%), Positives = 59/139 (42%), Gaps = 35/139 (25%)
Query: 220 KKRKEQLKRLFERTPEQVEEEQMLLAELKKIEIRRKERDRKTQDLQKLMTAADMQADNRK 279
+ K+QL L E++E+ + +AEL+ E+ + D Q L++L+ +
Sbjct: 82 SELKQQLSEL----QEELEDLEERIAELES-ELEDLKEDL--QLLRELLKSL-------- 126
Query: 280 TDKKMPPKRKLTHQIRPRSLDTSVKTTAFQTLIDLGLNPIPTEEIVTHYNELRSDMVLLY 339
+ R SL+ S+K A + L +L +++ ELR ++ L
Sbjct: 127 -------------EERLESLEESIKELA-KELREL------RQDLREEVEELREELERLQ 166
Query: 340 ELKQALDNYQFELQSLKHQ 358
E Q L ELQSL Q
Sbjct: 167 ENLQRLQEAIQELQSLLEQ 185
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 31.2 bits (71), Expect = 2.8
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 217 EHEKKRKE--QLKRLFERTPEQVEEEQMLLAE----LKKIEIRRKERDRKTQDLQKLMTA 270
E+E+ R+E +L R ++EE + E L+K++ +ER++ ++L+KL A
Sbjct: 660 EYEELREEYLELSRELAGLRAELEELEKRREEIKKTLEKLKEELEEREKAKKELEKLEKA 719
Query: 271 ADMQADNRKTDKK 283
+ + R+ KK
Sbjct: 720 LERVEELREKVKK 732
Score = 30.4 bits (69), Expect = 4.9
Identities = 12/47 (25%), Positives = 27/47 (57%)
Query: 220 KKRKEQLKRLFERTPEQVEEEQMLLAELKKIEIRRKERDRKTQDLQK 266
+K ++L+ L E E +E + L +K+E + +E + + ++L+K
Sbjct: 227 EKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKK 273
>gnl|CDD|206034 pfam13863, DUF4200, Domain of unknown function (DUF4200). This
family is found in eukaryotes. It is a coiled-coil
domain of unknwon function.
Length = 126
Score = 29.5 bits (67), Expect = 2.9
Identities = 19/96 (19%), Positives = 43/96 (44%), Gaps = 22/96 (22%)
Query: 210 EPKLFDAEHEKKRKE--QLKRLFERTPEQVEEEQMLLAE-------------------LK 248
E + + KR+E + + L ++ E++E+++ L E K
Sbjct: 8 EMEEVQLALDAKREEFERREELLKQREEELEKKEEELQESLIKFDKFLKENEAKRRRAEK 67
Query: 249 KIEIRRKERDRKTQDLQKLMTA-ADMQADNRKTDKK 283
K E +K R K +++++L +++A+ K ++K
Sbjct: 68 KAEEEKKLRKEKEEEIKELKAELEELKAEIEKLEEK 103
>gnl|CDD|224259 COG1340, COG1340, Uncharacterized archaeal coiled-coil protein
[Function unknown].
Length = 294
Score = 30.4 bits (69), Expect = 3.0
Identities = 32/164 (19%), Positives = 64/164 (39%), Gaps = 33/164 (20%)
Query: 217 EHEKKRKE-----------------QLKRLFERTPEQVEEEQMLLAELKKIEIRRKERDR 259
E ++KR E +++ L E+ E EE + E+++++ +R E +
Sbjct: 24 ELKEKRDELRKEASELAEKRDELNAKVRELREKAQELREERDEINEEVQELKEKRDEINA 83
Query: 260 KTQDLQKLMTAADMQADNRKTDKKMPPKRKLTHQIRPRSLDTSVKTTAFQTLIDLGLNPI 319
K Q+L+K +++ + + + L +I L+ QT + L P
Sbjct: 84 KLQELRK--EYRELKEKRNEFNLGGRSIKSLEREI--ERLE-----KKQQTSV---LTPE 131
Query: 320 PTEEIVTHYNELRSDMVLLYELKQALDNYQFELQSLKHQYEAVH 363
E+V ELR E + +L+ LK + + +
Sbjct: 132 EERELVQKIKELRK----ELEDAKKALEENEKLKELKAEIDELK 171
>gnl|CDD|205270 pfam13089, PP_kinase_N, Polyphosphate kinase N-terminal domain.
Polyphosphate kinase (Ppk) catalyzes the formation of
polyphosphate from ATP, with chain lengths of up to a
thousand or more orthophosphate molecules.
Length = 109
Score = 28.9 bits (66), Expect = 3.2
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 223 KEQLKRLFERTPEQVEE-----EQMLLAELKK--IEIRR 254
EQL+ + E+ E VEE + LL EL K I I R
Sbjct: 71 SEQLEAISEKVHELVEEQYRILNESLLPELAKEGIHILR 109
>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal
domain. This domain is found in a number of different
types of plant proteins including NAM-like proteins.
Length = 147
Score = 29.6 bits (67), Expect = 3.6
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 13/63 (20%)
Query: 220 KKRKEQLKR----------LFERTPEQVEEEQMLLAELKKIEIRRK--ERDRKTQDLQKL 267
KK KE+L+R E+ E+ + + AE ++ E+ +K E ++ +K+
Sbjct: 66 KKAKEKLRRDKLKAKKEEAEKEKEKEERFMKALAEAEKERAELEKKKAEAKLMKEE-KKI 124
Query: 268 MTA 270
M A
Sbjct: 125 MFA 127
>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572). Family of
eukaryotic proteins with undetermined function.
Length = 321
Score = 30.1 bits (68), Expect = 4.7
Identities = 21/111 (18%), Positives = 43/111 (38%), Gaps = 13/111 (11%)
Query: 210 EPKLFDAEHEKKRKEQLKRLFE--RTPEQVEEEQMLLAELKKIEIRRKERDRKTQDLQKL 267
E + D++ E + E+L+ L E V+ ML A ++ + +E + + + L K
Sbjct: 138 ENRTADSKREMEVLERLEELKELQSRRADVDVNSMLEALFRREKKEEEEEEEEDEALIKS 197
Query: 268 MT-----------AADMQADNRKTDKKMPPKRKLTHQIRPRSLDTSVKTTA 307
++ A D +++ + D P K + K+ A
Sbjct: 198 LSFGPETEEDRRRADDEDSEDDEEDNDNTPSPKSGSSSPAKPTSILKKSAA 248
>gnl|CDD|214018 cd12925, iSH2_PIK3R3, Inter-Src homology 2 (iSH2) helical domain of
Class IA Phosphoinositide 3-kinase Regulatory subunit 3,
PIK3R3, also called p55gamma. PI3Ks catalyze the
transfer of the gamma-phosphoryl group from ATP to the
3-hydroxyl of the inositol ring of
D-myo-phosphatidylinositol (PtdIns) or its derivatives.
They play an important role in a variety of fundamental
cellular processes, including cell motility, the Ras
pathway, vesicle trafficking and secretion, immune cell
activation, and apoptosis. They are classified according
to their substrate specificity, regulation, and domain
structure. Class IA PI3Ks are heterodimers of a p110
catalytic (C) subunit and a p85-related regulatory (R)
subunit. The R subunit down-regulates PI3K basal
activity, stabilizes the C subunit, and plays a role in
the activation downstream of tyrosine kinases. All R
subunits contain two SH2 domains that flank an
intervening helical domain (iSH2), which binds to the
N-terminal adaptor-binding domain (ABD) of the catalytic
subunit. p55gamma, also called PIK3R3 or p55PIK, also
contains a unique N-terminal 24-amino acid residue (N24)
that interacts with cell cycle modulators to promote
cell cycle progression.
Length = 161
Score = 29.3 bits (65), Expect = 4.9
Identities = 30/91 (32%), Positives = 48/91 (52%), Gaps = 10/91 (10%)
Query: 199 KMRGTECSGGNEP-KLFDAE---HEKKRKEQLKRLFERTPEQVEEEQMLLAELKKIEIRR 254
+M+ T NE K+F+ + E+ KE ++R F R + E E++++ +K++ R
Sbjct: 39 QMKRTAIEAFNETIKIFEEQCHTQERYSKEYIER-FRREGNEKEIERIMM-NYEKLKSRL 96
Query: 255 KE-RDRKTQDLQKLMTAADMQADNRKTDKKM 284
E D K + Q L T A DNR+ DKKM
Sbjct: 97 GEIHDSKMRLEQDLKTQA---LDNREIDKKM 124
>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional.
Length = 1021
Score = 30.1 bits (67), Expect = 5.3
Identities = 20/45 (44%), Positives = 30/45 (66%), Gaps = 3/45 (6%)
Query: 219 EKKRKEQLKRLFERTPEQVEEEQMLLAELKKIEIRRKERDRKTQD 263
EKKR E+L+R ER E++E E+M E +++E R ER+R +D
Sbjct: 456 EKKRIERLERE-ER--ERLERERMERIERERLERERLERERLERD 497
>gnl|CDD|192481 pfam10197, Cir_N, N-terminal domain of CBF1 interacting
co-repressor CIR. This is a 45 residue conserved region
at the N-terminal end of a family of proteins referred
to as CIRs (CBF1-interacting co-repressors). CBF1
(centromere-binding factor 1) acts as a transcription
factor that causes repression by binding specifically to
GTGGGAA motifs in responsive promoters, and it requires
CIR as a co-repressor. CIR binds to histone deacetylase
and to SAP30 and serves as a linker between CBF1 and the
histone deacetylase complex.
Length = 37
Score = 26.4 bits (59), Expect = 5.3
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 238 EEEQMLLAELKKIEIRRKERDR 259
E EQ L E KKIE RKE +
Sbjct: 15 EAEQKALEEQKKIEELRKEIEE 36
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 30.1 bits (68), Expect = 5.4
Identities = 36/184 (19%), Positives = 67/184 (36%), Gaps = 21/184 (11%)
Query: 215 DAEHEKKRKEQLKRLFERTPEQV--EEEQMLLAELKKIEIRRKERDRKTQDLQKLMTAAD 272
E + E+L+ L E+ Q EE + L L++++ E R + ++ +
Sbjct: 534 KLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELK-ELLEELRLLRTRKEELEELR 592
Query: 273 MQADNRKTDKKMPPKRKLTHQIRPRSLDTSVKTTAFQTLIDLGLNPIPTEEIVTHYNELR 332
+ K K +R + +SL+ S + EE+
Sbjct: 593 ERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAE---------EEL----ESEL 639
Query: 333 SDMVLLYELKQALDNYQFELQSLKHQYEAVHPGETFQIPEKIFEPTSLLSNLGDTEYL-Q 391
+ L EL++ L EL+ + EA E + ++I L L + E L +
Sbjct: 640 EKLNLQAELEELLQAALEELEEKVEELEA----EIRRELQRIENEEQLEEKLEELEQLEE 695
Query: 392 ELQS 395
EL+
Sbjct: 696 ELEQ 699
>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355). This
family of proteins is found in bacteria and viruses.
Proteins in this family are typically between 180 and
214 amino acids in length.
Length = 125
Score = 28.4 bits (64), Expect = 7.0
Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 14/79 (17%)
Query: 212 KLFDAEHEKKRKEQLKRLFERTPEQVEEEQMLLAELKKIEIRRKERDRKTQDLQKLM--- 268
K E K K+Q E+ + E LA++ E E ++ ++L++L
Sbjct: 15 KAIAKEKAKWEKKQ---------EEKKSEAEKLAKMSAEEKAEYELEKLEKELEELEAEL 65
Query: 269 TAADMQADNRK--TDKKMP 285
+++A+ +K ++K +P
Sbjct: 66 ARRELKAEAKKMLSEKGLP 84
>gnl|CDD|185040 PRK15082, PRK15082, glutathione ABC transporter permease GsiD;
Provisional.
Length = 301
Score = 29.3 bits (66), Expect = 7.2
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 301 TSVKTTAFQTLIDLGLNPIPTEEIVTHYNELRSDMVL 337
TS+ T A + + LG P PT E NE R+DMV+
Sbjct: 230 TSIITAASLSFLGLGAQP-PTPEWGAMLNEARADMVI 265
>gnl|CDD|238365 cd00713, GltS, Glutamine amidotransferases class-II (Gn-AT),
glutamate synthase (GltS)-type. GltS is a homodimer that
synthesizes L-glutamate from 2-oxoglutarate and
L-glutamine, an important step in ammonia assimilation
in bacteria, cyanobacteria and plants. The N-terminal
glutaminase domain catalyzes the hydrolysis of glutamine
to glutamic acid and ammonia, and has a fold similar to
that of other glutamine amidotransferases such as
glucosamine-fructose 6-phosphate synthase (GLMS or
GFAT), glutamine phosphoribosylpyrophosphate (Prpp)
amidotransferase (GPATase), asparagine synthetase B
(AsnB), and beta lactam synthetase (beta-LS), as well as
the Ntn hydrolase folds of the proteasomal alpha and
beta subunits.
Length = 413
Score = 29.4 bits (67), Expect = 7.3
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 156 DLCH-RFDLRFIVIHDRYDTNKFPTSRTIEDLKQRYYFVCH 195
DL RF+ F ++H R+ TN FP+ L Q + ++ H
Sbjct: 193 DLQDPRFESAFALVHSRFSTNTFPSW----PLAQPFRYLAH 229
>gnl|CDD|192445 pfam10018, Med4, Vitamin-D-receptor interacting Mediator subunit 4.
Members of this family function as part of the Mediator
(Med) complex, which links DNA-bound transcriptional
regulators and the general transcription machinery,
particularly the RNA polymerase II enzyme. They play a
role in basal transcription by mediating activation or
repression according to the specific complement of
transcriptional regulators bound to the promoter.
Length = 176
Score = 28.9 bits (65), Expect = 7.4
Identities = 19/127 (14%), Positives = 41/127 (32%), Gaps = 24/127 (18%)
Query: 235 EQVEEEQMLLAELKKIEIRRKERDRKTQDLQK------------LMTAADMQADNRKTDK 282
+++EE Q + ++ + D K +D+ K ++ +A+ RK
Sbjct: 19 KELEEHQENQQRILELRAEVESLDEKIKDILKELKEAEKELRTLPDLSSINKANKRKVSS 78
Query: 283 KMPPK--RKL---THQIRPRSLDTSVKTTAFQTLIDLGLNPIPTEEIVTHYNELRSDMVL 337
+ K ++ T S + + P P E+ E+R ++
Sbjct: 79 EELLKYAHRISKFTSAPPTVSSGAIAPNN-WIAPLGDLFRPWPAED------EMRRGLLA 131
Query: 338 LYELKQA 344
L
Sbjct: 132 QSSLLSK 138
>gnl|CDD|225394 COG2838, Icd, Monomeric isocitrate dehydrogenase [Energy production
and conversion].
Length = 744
Score = 29.4 bits (66), Expect = 8.2
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 582 FNINIAWSGALNPPMGDAEYLAAFRTIVMPVAKEFDPQIVLVSAGFDAAAGHPPPLGGY 640
F + + W+ L DAE A F P+AK + A +A G P +GGY
Sbjct: 663 FYLAMYWAQELAAQTEDAELAAHFA----PLAKALTENEAKIVAELNAVQGKPVDIGGY 717
>gnl|CDD|233560 TIGR01760, tape_meas_TP901, phage tail tape measure protein, TP901
family, core region. This model represents a reasonably
well conserved core region of a family of phage tail
proteins. The member from phage TP901-1 was
characterized as a tail length tape measure protein in
that a shortened form of the protein leads to phage with
proportionately shorter tails [Mobile and
extrachromosomal element functions, Prophage functions].
Length = 350
Score = 29.2 bits (66), Expect = 8.7
Identities = 13/63 (20%), Positives = 25/63 (39%)
Query: 215 DAEHEKKRKEQLKRLFERTPEQVEEEQMLLAELKKIEIRRKERDRKTQDLQKLMTAADMQ 274
++ + Q + L + TP + + L + I K+ T KL A+D+
Sbjct: 33 GSKEFEDLSNQARDLGDETPFSATQIAGAMTALARAGISAKDLLGATPTALKLAAASDLT 92
Query: 275 ADN 277
A+
Sbjct: 93 AEE 95
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.7 bits (66), Expect = 8.7
Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 4/78 (5%)
Query: 216 AEHEKKRKEQLKRLFE-RTPEQVE--EEQMLLAELKKIEIRRK-ERDRKTQDLQKLMTAA 271
A KK+ ++ K+ E + ++ + EE E KK E ++K + +K ++L+K
Sbjct: 1505 AAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKK 1564
Query: 272 DMQADNRKTDKKMPPKRK 289
+ + + K RK
Sbjct: 1565 KAEEAKKAEEDKNMALRK 1582
Score = 29.3 bits (65), Expect = 9.8
Identities = 19/82 (23%), Positives = 37/82 (45%)
Query: 217 EHEKKRKEQLKRLFERTPEQVEEEQMLLAELKKIEIRRKERDRKTQDLQKLMTAADMQAD 276
E K + E+ K+ E ++ EE + E KKI +KE ++K ++++K A +
Sbjct: 1726 EENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEEL 1785
Query: 277 NRKTDKKMPPKRKLTHQIRPRS 298
+ + +K+ K I
Sbjct: 1786 DEEDEKRRMEVDKKIKDIFDNF 1807
>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family. The organisation of
microtubules varies with the cell type and is presumably
controlled by tissue-specific microtubule-associated
proteins (MAPs). The 115-kDa epithelial MAP
(E-MAP-115/MAP7) has been identified as a
microtubule-stabilising protein predominantly expressed
in cell lines of epithelial origin. The binding of this
microtubule associated protein is nucleotide
independent.
Length = 171
Score = 28.5 bits (63), Expect = 8.8
Identities = 19/86 (22%), Positives = 40/86 (46%), Gaps = 4/86 (4%)
Query: 216 AEHEKKRKEQLKRLFERTPEQVEEEQMLLAELKKI----EIRRKERDRKTQDLQKLMTAA 271
A +++++EQ +R E EE A +++ E RR+E +R + +K A
Sbjct: 35 AREQREQEEQERREQEEQDRLEREELKRRAAEERLRREEEARRQEEERAREKEEKAKRKA 94
Query: 272 DMQADNRKTDKKMPPKRKLTHQIRPR 297
+ + + +++ K+K + R R
Sbjct: 95 EEEEKQEQEEQERIQKQKEEAEARAR 120
>gnl|CDD|219882 pfam08524, rRNA_processing, rRNA processing. This is a family of
proteins that are involved in rRNA processing. In a
localisation study they were found to localise to the
nucleus and nucleolus. The family also includes other
metazoa members from plants to mammals where the protein
has been named BR22 and is associated with TTF-1,
thyroid transcription factor 1. In the lungs, the family
binds TTF-1 to form a complex which influences the
expression of the key lung surfactant protein-B (SP-B)
and -C (SP-C), the small hydrophobic surfactant proteins
that maintain surface tension in alveoli.
Length = 150
Score = 28.3 bits (63), Expect = 9.1
Identities = 21/54 (38%), Positives = 33/54 (61%), Gaps = 6/54 (11%)
Query: 219 EKKRK--EQLKRLFERTPEQVEEEQMLL-AELKKIEI---RRKERDRKTQDLQK 266
EKK+K E+ + +R EQ E+E EL+KIE+ ++KER+R+ + L K
Sbjct: 69 EKKKKLDEKKEIAKQRKREQREKELAKRQKELEKIELSKKKQKERERRRKKLTK 122
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 29.3 bits (66), Expect = 9.2
Identities = 42/176 (23%), Positives = 73/176 (41%), Gaps = 28/176 (15%)
Query: 196 TLAKMRGTECSGGNEPKLFDAEHEKKRKEQLKRLFERTPEQVEEEQMLLAELK------- 248
K+ TE N +L D E ++ QL++L ER E+ E Q L AEL+
Sbjct: 177 AERKLERTE---ENLERLEDLLEELEK--QLEKL-ERQAEKAERYQELKAELRELELALL 230
Query: 249 --KIEIRRKERDRKTQDLQKLMT-AADMQADNRKTDKKMPPKRKLTHQIRPRSLDTSVKT 305
K++ RKE + ++L +L ++Q + + +K++ + ++R +
Sbjct: 231 LAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEE---LQ 287
Query: 306 TAFQTLIDLGLNPIPTEEIVTHYNELRSDMVLLYELKQALDNYQFELQSLKHQYEA 361
L EEI E+ L EL+ L+ + L+ LK + EA
Sbjct: 288 EELLEL---------KEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEA 334
>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family. This family of
proteins contain a band 4.1 domain (pfam00373), at their
amino terminus. This family represents the rest of these
proteins.
Length = 244
Score = 28.9 bits (65), Expect = 9.4
Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 1/73 (1%)
Query: 210 EPKLFDAEHEKKRKEQLKRLFERTPEQVEEEQMLLAELK-KIEIRRKERDRKTQDLQKLM 268
E KL E E + E+ E ++EEE E + ++E E + L++
Sbjct: 39 EEKLKQEEEEAQLLEKKADELEEENRRLEEEAAASEEERERLEAEVDEATAEVAKLEEER 98
Query: 269 TAADMQADNRKTD 281
+ + + +
Sbjct: 99 EKKEAETRQLQQE 111
>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa). Members of this
family of proteins are part of the yeast nuclear pore
complex-associated pre-60S ribosomal subunit. The family
functions as a highly conserved exonuclease that is
required for the 5'-end maturation of 5.8S and 25S
rRNAs, demonstrating that 5'-end processing also has a
redundant pathway. Nop25 binds late pre-60S ribosomes,
accompanying them from the nucleolus to the nuclear
periphery; and there is evidence for both physical and
functional links between late 60S subunit processing and
export.
Length = 134
Score = 28.1 bits (63), Expect = 9.5
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 12/61 (19%)
Query: 214 FDAEHEKKRKEQL----KRLFERTPEQVE--EEQMLLAELKKIEIRRKERDRKTQDLQKL 267
FD ++ RKE L KR +R + E +E+ ++IE R++ R+ + Q+L+K
Sbjct: 15 FD---KEARKEYLTGFHKRKQQRRKKAQEEAKEK---EREERIEERKRIREERKQELEKQ 68
Query: 268 M 268
+
Sbjct: 69 L 69
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 29.2 bits (66), Expect = 9.6
Identities = 32/156 (20%), Positives = 61/156 (39%), Gaps = 23/156 (14%)
Query: 222 RKEQLKRLFERTPEQVEEE------------QMLLAELKKI---EIRRKERDRKTQDLQK 266
RK +L+ F+ +++ E+ + L EL+ I E E ++L+
Sbjct: 268 RKAELEAHFDEEYQELIEQLEELIDKYESHIEKALEELESILDTEKENSEFKLDVEELKA 327
Query: 267 LMTAADMQAD-NRK--TDKKMPPKRKLT-HQIRPRSLDTSVKTTAFQTLIDLGLNPIPTE 322
L+ A + + N + +K P + I + A LI N +
Sbjct: 328 LLEALEEILEKNLQKLEEKLKDPSTSIELESITDLIESINDIIDAINELIRE-HNEK-ID 385
Query: 323 EIVTHYNELRSDMVL--LYELKQALDNYQFELQSLK 356
+ N+ + + L + ELK+ +D YQ E + L+
Sbjct: 386 NLKKEKNKAKKKLWLHLVAELKEDIDAYQKEKKGLE 421
>gnl|CDD|197400 cd10164, ClassIIa_HDAC5_Gln-rich-N, Glutamine-rich N-terminal
helical domain of HDAC5, a Class IIa histone
deacetylase. This family consists of the glutamine-rich
domain of histone deacetylase 5 (HDAC5). It belongs to a
superfamily that consists of the glutamine-rich
N-terminal helical extension to certain Class IIa
histone deacetylases (HDACs), including HDAC4, HDAC5 and
HDCA9; it is missing from HDAC7. This domain confers
responsiveness to calcium signals and mediates
interactions with transcription factors and cofactors,
and it is able to repress transcription independently of
the HDAC C-terminal, zinc-dependent catalytic domain. It
has many intra- and inter-helical interactions which are
possibly involved in reversible assembly and disassembly
of proteins. HDACs regulate diverse cellular processes
through enzymatic deacetylation of histone as well as
non-histone proteins, in particular deacetylating
N(6)-acetyl-lysine residues.
Length = 97
Score = 27.5 bits (60), Expect = 9.7
Identities = 13/50 (26%), Positives = 29/50 (58%)
Query: 217 EHEKKRKEQLKRLFERTPEQVEEEQMLLAELKKIEIRRKERDRKTQDLQK 266
+HE + ++ LK E EQ ++E + +++E +RK ++ ++L+K
Sbjct: 41 QHEVQLQKHLKVRAELFSEQQQQEILAAKRQQELEQQRKREQQRQEELEK 90
>gnl|CDD|237418 PRK13534, PRK13534, 7-cyano-7-deazaguanine tRNA-ribosyltransferase;
Provisional.
Length = 639
Score = 29.2 bits (66), Expect = 9.8
Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 9/90 (10%)
Query: 211 PKLFDAEHEKKRKEQLKRLFERTPEQVEEEQMLLAELKKIEIRRKERDRKTQDLQKLMTA 270
P+LFD E ++ E + E++ + + + K D DL ++
Sbjct: 441 PELFDYEGKEFNNEFVSEFKVIIHEKILDILTYNYYINHYGEKPKIND----DLLRIRAI 496
Query: 271 ADMQ-----ADNRKTDKKMPPKRKLTHQIR 295
A+ Q D DK + K T +IR
Sbjct: 497 AEYQFGEGAGDAEFFDKVKIERSKKTGRIR 526
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.412
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 40,445,578
Number of extensions: 4050258
Number of successful extensions: 4578
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4427
Number of HSP's successfully gapped: 165
Length of query: 774
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 670
Effective length of database: 6,324,786
Effective search space: 4237606620
Effective search space used: 4237606620
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 63 (28.1 bits)